Mapping the human genome entails localizing and ordering DNA sequences on the chromosomes. Probe sequences are generally short, e.g. 2-4Kb, and there are well-established statistical methods for the analysis of short probes. Recently, the placement of longer DNA sequences, such as 250Kb YACs or 1Mb MegaYACs, has become important in the physical mapping chromosomes. However, the established statistical methods are not applicable to these larger probes. This proposal introduces a new chromosome mapping approach termed Inner Product Mapping (IPM), which can be used for mapping DNA sequences of any size. Inner Product Mapping of a chromosome uses the standard table of radiation hybrid versus probe comparisons, together with a table that characterizes where radiation hybrid fragments reside on the chromosome. These two data tables can be experimentally determined at relatively low cost. When the tables are multiplied together as matrices under a suitable inner product, the chromosome map of the markers is generated. We propose to determine the effectiveness and utility of the IPM algorithm, and to develop software that assists investigators in the use of IPM.